Note
Go to the end to download the full example code
8.7. Run junifer and julearn.#
This example uses a ParcelAggregation marker to compute the mean of each parcel using the Schaefer parcellation (100 rois, 7 Yeo networks) for a 3D nifti to extract some features for machine learning using julearn to predict some other data.
Authors: Leonard Sasse, Sami Hamdan, Nicolas Nieto, Synchon Mandal
License: BSD 3 clause
import tempfile
import nilearn
import pandas as pd
from julearn import run_cross_validation, PipelineCreator
import junifer.testing.registry # noqa: F401
from junifer.api import collect, run
from junifer.storage.sqlite import SQLiteFeatureStorage
from junifer.utils import configure_logging
Set the logging level to info to see extra information:
configure_logging(level="INFO")
2024-04-30 13:12:56,891 - JUNIFER - INFO - ===== Lib Versions =====
2024-04-30 13:12:56,891 - JUNIFER - INFO - numpy: 1.26.4
2024-04-30 13:12:56,891 - JUNIFER - INFO - scipy: 1.11.4
2024-04-30 13:12:56,891 - JUNIFER - INFO - pandas: 2.1.4
2024-04-30 13:12:56,891 - JUNIFER - INFO - nilearn: 0.10.2
2024-04-30 13:12:56,891 - JUNIFER - INFO - nibabel: 5.2.1
2024-04-30 13:12:56,891 - JUNIFER - INFO - junifer: 0.0.5.dev48
2024-04-30 13:12:56,891 - JUNIFER - INFO - ========================
Define the markers you want:
marker_dicts = [
{
"name": "Schaefer100x17_TrimMean80",
"kind": "ParcelAggregation",
"parcellation": "Schaefer100x17",
"method": "trim_mean",
"method_params": {"proportiontocut": 0.2},
},
{
"name": "Schaefer200x17_Mean",
"kind": "ParcelAggregation",
"parcellation": "Schaefer200x17",
"method": "mean",
},
]
Define target and confounds for julearn machine learning:
Load the VBM phenotype data for machine learning data: - Fetch the Oasis dataset
oasis_dataset = nilearn.datasets.fetch_oasis_vbm()
age = oasis_dataset.ext_vars[y][:10]
sex = (
pd.Series(oasis_dataset.ext_vars["mf"][:10])
.map(lambda x: 1 if x == "F" else 0)
.values
)
/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/nilearn/datasets/struct.py:852: UserWarning: `legacy_format` will default to `False` in release 0.11. Dataset fetchers will then return pandas dataframes by default instead of recarrays.
warnings.warn(_LEGACY_FORMAT_MSG)
Create a temporary directory for junifer feature extraction:
with tempfile.TemporaryDirectory() as tmpdir:
storage = {"kind": "SQLiteFeatureStorage", "uri": f"{tmpdir}/test.sqlite"}
# run the defined junifer feature extraction pipeline
run(
workdir="/tmp",
datagrabber={"kind": "OasisVBMTestingDataGrabber"},
markers=marker_dicts,
storage=storage,
)
# read in extracted features and add confounds and targets
# for julearn run cross validation
collect(storage)
db = SQLiteFeatureStorage(uri=storage["uri"])
df_vbm = db.read_df(feature_name="VBM_GM_Schaefer200x17_Mean")
oasis_subjects = [x[0] for x in df_vbm.index]
df_vbm.index = oasis_subjects
2024-04-30 13:12:56,904 - JUNIFER - INFO - Validating Marker Collection
2024-04-30 13:12:56,904 - JUNIFER - INFO - DataGrabber output type: ['VBM_GM']
2024-04-30 13:12:56,904 - JUNIFER - INFO - Validating Data Reader:
2024-04-30 13:12:56,905 - JUNIFER - INFO - Data Reader output type: ['VBM_GM']
2024-04-30 13:12:56,905 - JUNIFER - INFO - Validating Marker: Schaefer100x17_TrimMean80
2024-04-30 13:12:56,905 - JUNIFER - INFO - Marker output type: ['vector']
2024-04-30 13:12:56,905 - JUNIFER - INFO - Validating storage for Schaefer100x17_TrimMean80
2024-04-30 13:12:56,905 - JUNIFER - INFO - Validating Marker: Schaefer200x17_Mean
2024-04-30 13:12:56,905 - JUNIFER - INFO - Marker output type: ['vector']
2024-04-30 13:12:56,905 - JUNIFER - INFO - Validating storage for Schaefer200x17_Mean
/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/nilearn/datasets/struct.py:852: UserWarning: `legacy_format` will default to `False` in release 0.11. Dataset fetchers will then return pandas dataframes by default instead of recarrays.
warnings.warn(_LEGACY_FORMAT_MSG)
2024-04-30 13:12:56,909 - JUNIFER - INFO - Getting element sub-01
2024-04-30 13:12:56,909 - JUNIFER - INFO - Fitting pipeline
2024-04-30 13:12:56,909 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-30 13:12:56,909 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-30 13:12:56,910 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-04-30 13:12:56,910 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:12:56,910 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:12:56,910 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:12:56,910 - JUNIFER - INFO - resolution: 2.0
2024-04-30 13:12:56,910 - JUNIFER - INFO - n_rois: 100
2024-04-30 13:12:56,910 - JUNIFER - INFO - yeo_networks: 17
2024-04-30 13:12:56,911 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:12:56,941 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:12:58,002 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:12:58,098 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellations0xp7s_xg/Schaefer100x17.nii.gz -r /tmp/tmp1q1papv3/parcellations0xp7s_xg/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpgh7b8iw2/parcellationsiu8d5he9/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:12:59,492 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:13:00,458 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5txa9bdt/test.sqlite (multiple output)>
2024-04-30 13:13:00,491 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-04-30 13:13:00,491 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:13:00,491 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:13:00,492 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:13:00,492 - JUNIFER - INFO - resolution: 2.0
2024-04-30 13:13:00,492 - JUNIFER - INFO - n_rois: 200
2024-04-30 13:13:00,492 - JUNIFER - INFO - yeo_networks: 17
2024-04-30 13:13:00,493 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:13:00,523 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:13:01,579 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:13:01,675 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellations_0axrbnh/Schaefer200x17.nii.gz -r /tmp/tmp1q1papv3/parcellations_0axrbnh/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpgh7b8iw2/parcellationsq_cv_0wr/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:13:03,679 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:13:04,623 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5txa9bdt/test.sqlite (multiple output)>
2024-04-30 13:13:04,670 - JUNIFER - INFO - Marker collection fitting done
2024-04-30 13:13:04,670 - JUNIFER - INFO - Getting element sub-02
2024-04-30 13:13:04,670 - JUNIFER - INFO - Fitting pipeline
2024-04-30 13:13:04,670 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-30 13:13:04,670 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-30 13:13:04,671 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-04-30 13:13:04,671 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:13:04,671 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:13:04,671 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:13:04,672 - JUNIFER - INFO - resolution: 2.0
2024-04-30 13:13:04,672 - JUNIFER - INFO - n_rois: 100
2024-04-30 13:13:04,672 - JUNIFER - INFO - yeo_networks: 17
2024-04-30 13:13:04,673 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:13:04,703 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:13:05,747 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:13:05,844 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellations5t0vye7l/Schaefer100x17.nii.gz -r /tmp/tmp1q1papv3/parcellations5t0vye7l/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpd799nvpv/parcellations1c28vhy6/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:13:07,249 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:13:08,160 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5txa9bdt/test.sqlite (multiple output)>
2024-04-30 13:13:08,191 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-04-30 13:13:08,191 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:13:08,191 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:13:08,191 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:13:08,191 - JUNIFER - INFO - resolution: 2.0
2024-04-30 13:13:08,192 - JUNIFER - INFO - n_rois: 200
2024-04-30 13:13:08,192 - JUNIFER - INFO - yeo_networks: 17
2024-04-30 13:13:08,193 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:13:08,223 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:13:09,292 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:13:09,389 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationsvrtytq3y/Schaefer200x17.nii.gz -r /tmp/tmp1q1papv3/parcellationsvrtytq3y/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpd799nvpv/parcellations3r7web48/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:13:11,404 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:13:12,340 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5txa9bdt/test.sqlite (multiple output)>
2024-04-30 13:13:12,388 - JUNIFER - INFO - Marker collection fitting done
2024-04-30 13:13:12,388 - JUNIFER - INFO - Getting element sub-03
2024-04-30 13:13:12,388 - JUNIFER - INFO - Fitting pipeline
2024-04-30 13:13:12,388 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-30 13:13:12,388 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-30 13:13:12,389 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-04-30 13:13:12,389 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:13:12,389 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:13:12,390 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:13:12,390 - JUNIFER - INFO - resolution: 2.0
2024-04-30 13:13:12,390 - JUNIFER - INFO - n_rois: 100
2024-04-30 13:13:12,390 - JUNIFER - INFO - yeo_networks: 17
2024-04-30 13:13:12,391 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:13:12,421 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:13:13,488 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:13:13,584 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellations8w86tp5z/Schaefer100x17.nii.gz -r /tmp/tmp1q1papv3/parcellations8w86tp5z/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpgm7y06ox/parcellationsefyp5hdl/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:13:14,988 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:13:15,966 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5txa9bdt/test.sqlite (multiple output)>
2024-04-30 13:13:15,997 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-04-30 13:13:15,997 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:13:15,997 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:13:15,997 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:13:15,997 - JUNIFER - INFO - resolution: 2.0
2024-04-30 13:13:15,997 - JUNIFER - INFO - n_rois: 200
2024-04-30 13:13:15,997 - JUNIFER - INFO - yeo_networks: 17
2024-04-30 13:13:15,999 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:13:16,029 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:13:17,068 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:13:17,165 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationsq3uxc2_w/Schaefer200x17.nii.gz -r /tmp/tmp1q1papv3/parcellationsq3uxc2_w/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpgm7y06ox/parcellationsj24bk_ny/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:13:19,193 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:13:20,151 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5txa9bdt/test.sqlite (multiple output)>
2024-04-30 13:13:20,203 - JUNIFER - INFO - Marker collection fitting done
2024-04-30 13:13:20,203 - JUNIFER - INFO - Getting element sub-04
2024-04-30 13:13:20,203 - JUNIFER - INFO - Fitting pipeline
2024-04-30 13:13:20,204 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-30 13:13:20,204 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-30 13:13:20,204 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-04-30 13:13:20,204 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:13:20,205 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:13:20,205 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:13:20,205 - JUNIFER - INFO - resolution: 2.0
2024-04-30 13:13:20,205 - JUNIFER - INFO - n_rois: 100
2024-04-30 13:13:20,205 - JUNIFER - INFO - yeo_networks: 17
2024-04-30 13:13:20,206 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:13:20,236 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:13:21,318 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:13:21,414 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationsdtdy9t5k/Schaefer100x17.nii.gz -r /tmp/tmp1q1papv3/parcellationsdtdy9t5k/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp9vp4_0zo/parcellationsbokkkae8/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:13:22,814 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:13:23,757 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5txa9bdt/test.sqlite (multiple output)>
2024-04-30 13:13:23,791 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-04-30 13:13:23,792 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:13:23,792 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:13:23,792 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:13:23,792 - JUNIFER - INFO - resolution: 2.0
2024-04-30 13:13:23,792 - JUNIFER - INFO - n_rois: 200
2024-04-30 13:13:23,792 - JUNIFER - INFO - yeo_networks: 17
2024-04-30 13:13:23,793 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:13:23,824 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:13:24,889 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:13:24,986 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellations3wsotopv/Schaefer200x17.nii.gz -r /tmp/tmp1q1papv3/parcellations3wsotopv/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp9vp4_0zo/parcellationsdflucl2v/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:13:27,021 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:13:28,030 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5txa9bdt/test.sqlite (multiple output)>
2024-04-30 13:13:28,081 - JUNIFER - INFO - Marker collection fitting done
2024-04-30 13:13:28,082 - JUNIFER - INFO - Getting element sub-05
2024-04-30 13:13:28,082 - JUNIFER - INFO - Fitting pipeline
2024-04-30 13:13:28,082 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-30 13:13:28,082 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-30 13:13:28,083 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-04-30 13:13:28,083 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:13:28,083 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:13:28,083 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:13:28,083 - JUNIFER - INFO - resolution: 2.0
2024-04-30 13:13:28,083 - JUNIFER - INFO - n_rois: 100
2024-04-30 13:13:28,084 - JUNIFER - INFO - yeo_networks: 17
2024-04-30 13:13:28,085 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:13:28,115 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:13:29,175 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:13:29,271 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationsyzpcedok/Schaefer100x17.nii.gz -r /tmp/tmp1q1papv3/parcellationsyzpcedok/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp4mlr6au0/parcellations635yx8rv/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:13:30,675 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:13:31,605 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5txa9bdt/test.sqlite (multiple output)>
2024-04-30 13:13:31,640 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-04-30 13:13:31,640 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:13:31,641 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:13:31,641 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:13:31,641 - JUNIFER - INFO - resolution: 2.0
2024-04-30 13:13:31,641 - JUNIFER - INFO - n_rois: 200
2024-04-30 13:13:31,641 - JUNIFER - INFO - yeo_networks: 17
2024-04-30 13:13:31,642 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:13:31,673 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:13:32,723 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:13:32,821 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationsv2_k656h/Schaefer200x17.nii.gz -r /tmp/tmp1q1papv3/parcellationsv2_k656h/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp4mlr6au0/parcellationsrnlmqzlf/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:13:34,837 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:13:35,806 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5txa9bdt/test.sqlite (multiple output)>
2024-04-30 13:13:35,854 - JUNIFER - INFO - Marker collection fitting done
2024-04-30 13:13:35,854 - JUNIFER - INFO - Getting element sub-06
2024-04-30 13:13:35,854 - JUNIFER - INFO - Fitting pipeline
2024-04-30 13:13:35,854 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-30 13:13:35,854 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-30 13:13:35,855 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-04-30 13:13:35,855 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:13:35,855 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:13:35,855 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:13:35,855 - JUNIFER - INFO - resolution: 2.0
2024-04-30 13:13:35,856 - JUNIFER - INFO - n_rois: 100
2024-04-30 13:13:35,856 - JUNIFER - INFO - yeo_networks: 17
2024-04-30 13:13:35,857 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:13:35,886 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:13:36,940 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:13:37,036 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationsboyud9o9/Schaefer100x17.nii.gz -r /tmp/tmp1q1papv3/parcellationsboyud9o9/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmppk160b1q/parcellationslhykmr3h/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:13:38,420 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:13:39,347 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5txa9bdt/test.sqlite (multiple output)>
2024-04-30 13:13:39,378 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-04-30 13:13:39,378 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:13:39,378 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:13:39,379 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:13:39,379 - JUNIFER - INFO - resolution: 2.0
2024-04-30 13:13:39,379 - JUNIFER - INFO - n_rois: 200
2024-04-30 13:13:39,379 - JUNIFER - INFO - yeo_networks: 17
2024-04-30 13:13:39,380 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:13:39,410 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:13:40,467 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:13:40,564 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellations__q6afvb/Schaefer200x17.nii.gz -r /tmp/tmp1q1papv3/parcellations__q6afvb/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmppk160b1q/parcellationsb71sbi_8/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:13:42,568 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:13:43,487 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5txa9bdt/test.sqlite (multiple output)>
2024-04-30 13:13:43,534 - JUNIFER - INFO - Marker collection fitting done
2024-04-30 13:13:43,534 - JUNIFER - INFO - Getting element sub-07
2024-04-30 13:13:43,534 - JUNIFER - INFO - Fitting pipeline
2024-04-30 13:13:43,534 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-30 13:13:43,534 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-30 13:13:43,535 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-04-30 13:13:43,535 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:13:43,536 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:13:43,536 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:13:43,536 - JUNIFER - INFO - resolution: 2.0
2024-04-30 13:13:43,536 - JUNIFER - INFO - n_rois: 100
2024-04-30 13:13:43,536 - JUNIFER - INFO - yeo_networks: 17
2024-04-30 13:13:43,537 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:13:43,567 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:13:44,633 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:13:44,730 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationsbssihwve/Schaefer100x17.nii.gz -r /tmp/tmp1q1papv3/parcellationsbssihwve/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpaf78r55y/parcellationsik81377g/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:13:46,132 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:13:47,061 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5txa9bdt/test.sqlite (multiple output)>
2024-04-30 13:13:47,098 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-04-30 13:13:47,098 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:13:47,098 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:13:47,098 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:13:47,098 - JUNIFER - INFO - resolution: 2.0
2024-04-30 13:13:47,098 - JUNIFER - INFO - n_rois: 200
2024-04-30 13:13:47,098 - JUNIFER - INFO - yeo_networks: 17
2024-04-30 13:13:47,100 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:13:47,130 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:13:48,174 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:13:48,271 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationsx5_h95wx/Schaefer200x17.nii.gz -r /tmp/tmp1q1papv3/parcellationsx5_h95wx/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpaf78r55y/parcellationsrnm4ml6h/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:13:50,290 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:13:51,236 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5txa9bdt/test.sqlite (multiple output)>
2024-04-30 13:13:51,283 - JUNIFER - INFO - Marker collection fitting done
2024-04-30 13:13:51,284 - JUNIFER - INFO - Getting element sub-08
2024-04-30 13:13:51,284 - JUNIFER - INFO - Fitting pipeline
2024-04-30 13:13:51,284 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-30 13:13:51,284 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-30 13:13:51,285 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-04-30 13:13:51,285 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:13:51,285 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:13:51,285 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:13:51,285 - JUNIFER - INFO - resolution: 2.0
2024-04-30 13:13:51,285 - JUNIFER - INFO - n_rois: 100
2024-04-30 13:13:51,285 - JUNIFER - INFO - yeo_networks: 17
2024-04-30 13:13:51,286 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:13:51,316 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:13:52,380 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:13:52,476 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationsnhq4tgs4/Schaefer100x17.nii.gz -r /tmp/tmp1q1papv3/parcellationsnhq4tgs4/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpwfssymsi/parcellationsc4gb02_q/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:13:53,870 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:13:54,793 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5txa9bdt/test.sqlite (multiple output)>
2024-04-30 13:13:54,829 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-04-30 13:13:54,829 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:13:54,829 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:13:54,829 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:13:54,829 - JUNIFER - INFO - resolution: 2.0
2024-04-30 13:13:54,829 - JUNIFER - INFO - n_rois: 200
2024-04-30 13:13:54,829 - JUNIFER - INFO - yeo_networks: 17
2024-04-30 13:13:54,831 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:13:54,861 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:13:55,918 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:13:56,015 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationso9v64lb6/Schaefer200x17.nii.gz -r /tmp/tmp1q1papv3/parcellationso9v64lb6/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpwfssymsi/parcellations3t1ghx6e/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:13:58,041 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:13:58,988 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5txa9bdt/test.sqlite (multiple output)>
2024-04-30 13:13:59,036 - JUNIFER - INFO - Marker collection fitting done
2024-04-30 13:13:59,036 - JUNIFER - INFO - Getting element sub-09
2024-04-30 13:13:59,036 - JUNIFER - INFO - Fitting pipeline
2024-04-30 13:13:59,036 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-30 13:13:59,036 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-30 13:13:59,037 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-04-30 13:13:59,037 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:13:59,038 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:13:59,038 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:13:59,038 - JUNIFER - INFO - resolution: 2.0
2024-04-30 13:13:59,038 - JUNIFER - INFO - n_rois: 100
2024-04-30 13:13:59,038 - JUNIFER - INFO - yeo_networks: 17
2024-04-30 13:13:59,039 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:13:59,068 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:14:00,127 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:14:00,224 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellations1nut6hi7/Schaefer100x17.nii.gz -r /tmp/tmp1q1papv3/parcellations1nut6hi7/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpe667d0dq/parcellationspfpho5vf/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:14:01,617 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:14:02,579 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5txa9bdt/test.sqlite (multiple output)>
2024-04-30 13:14:02,610 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-04-30 13:14:02,610 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:14:02,610 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:14:02,610 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:14:02,610 - JUNIFER - INFO - resolution: 2.0
2024-04-30 13:14:02,610 - JUNIFER - INFO - n_rois: 200
2024-04-30 13:14:02,610 - JUNIFER - INFO - yeo_networks: 17
2024-04-30 13:14:02,612 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:14:02,642 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:14:03,688 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:14:03,785 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationst9agw2ra/Schaefer200x17.nii.gz -r /tmp/tmp1q1papv3/parcellationst9agw2ra/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpe667d0dq/parcellations_6sc_dys/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:14:05,815 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:14:06,762 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5txa9bdt/test.sqlite (multiple output)>
2024-04-30 13:14:06,808 - JUNIFER - INFO - Marker collection fitting done
2024-04-30 13:14:06,808 - JUNIFER - INFO - Getting element sub-10
2024-04-30 13:14:06,808 - JUNIFER - INFO - Fitting pipeline
2024-04-30 13:14:06,808 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-04-30 13:14:06,808 - JUNIFER - INFO - VBM_GM is type NIFTI
2024-04-30 13:14:06,809 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-04-30 13:14:06,809 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:14:06,810 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:14:06,810 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:14:06,810 - JUNIFER - INFO - resolution: 2.0
2024-04-30 13:14:06,810 - JUNIFER - INFO - n_rois: 100
2024-04-30 13:14:06,810 - JUNIFER - INFO - yeo_networks: 17
2024-04-30 13:14:06,811 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:14:06,840 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:14:07,890 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:14:07,986 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationsu_f5yzv5/Schaefer100x17.nii.gz -r /tmp/tmp1q1papv3/parcellationsu_f5yzv5/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpm5se07aq/parcellationsmg6jmtja/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:14:09,407 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:14:10,341 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5txa9bdt/test.sqlite (multiple output)>
2024-04-30 13:14:10,375 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-04-30 13:14:10,375 - JUNIFER - INFO - Computing VBM_GM
2024-04-30 13:14:10,375 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-04-30 13:14:10,375 - JUNIFER - INFO - Parcellation parameters:
2024-04-30 13:14:10,375 - JUNIFER - INFO - resolution: 2.0
2024-04-30 13:14:10,376 - JUNIFER - INFO - n_rois: 200
2024-04-30 13:14:10,376 - JUNIFER - INFO - yeo_networks: 17
2024-04-30 13:14:10,377 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-04-30 13:14:10,407 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-04-30 13:14:11,464 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-04-30 13:14:11,561 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmp1q1papv3/parcellationsz5g13fqv/Schaefer200x17.nii.gz -r /tmp/tmp1q1papv3/parcellationsz5g13fqv/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpm5se07aq/parcellations6ilflfv_/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-04-30 13:14:13,578 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
b''
2024-04-30 13:14:14,506 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmp5txa9bdt/test.sqlite (multiple output)>
2024-04-30 13:14:14,553 - JUNIFER - INFO - Marker collection fitting done
2024-04-30 13:14:14,553 - JUNIFER - INFO - Collecting data using SQLiteFeatureStorage
2024-04-30 13:14:14,553 - JUNIFER - INFO - Collecting data from /tmp/tmp5txa9bdt/*test.sqlite
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2024-04-30 13:14:16,087 - JUNIFER - INFO - Collect done
Using julearn for machine learning: We predict the age given our vbm features and sex as a confound.
X = list(df_vbm.columns)
df_vbm[y] = age
df_vbm[confound] = sex
X_types = {
"features": X,
"confound": confound,
}
creator = PipelineCreator(problem_type="regression", apply_to="features")
creator.add("zscore", apply_to=["features", "confound"])
creator.add("confound_removal", apply_to="features", confounds="confound")
creator.add("ridge")
scores = run_cross_validation(
X=X + [confound],
y=y,
X_types=X_types,
data=df_vbm,
model=creator,
cv=3,
)
print(scores)
fit_time score_time ... fold cv_mdsum
0 0.132308 0.018840 ... 0 509497eb21da473048117e0c6704d3ea
1 0.130454 0.018605 ... 1 509497eb21da473048117e0c6704d3ea
2 0.129455 0.018451 ... 2 509497eb21da473048117e0c6704d3ea
[3 rows x 8 columns]
Interpretation of results: Doing machine learning with only 10 datapoints is not meaningful. This explains the big variation in scores for different cross-validation folds.
Total running time of the script: (1 minutes 19.804 seconds)